The Complete Genome of an Endogenous Nimavirus (Nimav-1_LVa) From the Pacific Whiteleg Shrimp Penaeus (Litopenaeus) Vannamei

Abstract

White spot syndrome virus (WSSV), the lone virus of the genus Whispovirus under the family Nimaviridae, is one of the most devastating viruses affecting the shrimp farming industry. Knowledge about this virus, in particular, its evolution history, has been limited, partly due to its large genome and the lack of other closely related free-living viruses for comparative studies. In this study, we reconstructed a full-length endogenous nimavirus consensus genome, Nimav-1_LVa (279,905 bp), in the genome sequence of Penaeus (Litopenaeus) vannamei breed Kehai No. 1 (ASM378908v1). This endogenous virus seemed to insert exclusively into the telomeric pentanucleotide microsatellite (TAACC/GGTTA)n. It encoded 117 putative genes, with some containing introns, such as g012 (inhibitor of apoptosis, IAP), g046 (crustacean hyperglycemic hormone, CHH), g155 (innexin), g158 (Bax inhibitor 1 like). More than a dozen Nimav-1_LVa genes are involved in the pathogen-host interactions. We hypothesized that g046, g155, g158, and g227 (semaphorin 1A like) were recruited host genes for their roles in immune regulation. Sequence analysis indicated that a total of 43 WSSV genes belonged to the ancestral/core nimavirus gene set, including four genes reported in this study: wsv112 (dUTPase), wsv206, wsv226, and wsv308 (nucleocapsid protein). The availability of the Nimav-1_LVa sequence would help understand the genetic diversity, epidemiology, evolution, and virulence of WSSV.

Hallmarks of crustacean immune hemocytes at single-cell resolution

“…However, other markers of granular hemocytes, such as mannose-binding protein are negligibly detected in CC5, indicating CC5 might be immature granular hemocytes. Innexin, a gap junction protein, functions as an antiviral protein in Procambarus clarkia ( 43 ). Therefore, CC5 might be immature granular hemocytes involved in immune responses.…”

Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans

“…Despite the limited number of known exogenous nimaviruses, genomic analyses of decapod crustaceans have revealed the presence of sequences originating from nimaviruses (7)(8)(9)(10)(11). These endogenous viral elements (12,13) are present as multi-copy elements sometimes reaching hundreds of copies per haploid genome (7,10).…”

“…The earliest reportson WSSV-like sequences in the penaeid shrimp genomes noted an expansion of a large DNA segment containing WSSV homologs as well as various eukaryotic genes, including baculoviral inhibitor of apoptosis repeat (BIR)-containing proteins (7) and an HSP70 homolog (17). Bao et al also observed the presence of eukaryotic-like genes on the Nimav-1_LVa genome (11). The availability of complete majaniviral genomes confirms that the presence of eukaryotic-like genes is a shared trait of majaniviruses.…”

“…To recover both classes of proteincoding genes, we used different gene prediction programs and integrated the outputs into a nonredundant annotation. Open reading frames were predicted by Prodigal v2.6.3 (78), and the predicted proteins were queried against the proteomes of nimaviruses (11). The predicted proteins (generated by gffread ( 83)) were BLASTP searched against the abovementioned nimaviral and arthropod proteomes, and the BLASTP output were passed to AHRD to generate final functional annotations.…”

“…The genomic coordinates corresponding to nimaviral-like proteins were masked by BEDtools (81), and the remaining coordinates were forwarded to ab initio eukaryotic-like gene prediction by Augustus v3.3.3 (82) using the Apis mellifera gene model(11). The use of Apis mellifera gene model was inspired byBao et al (2020)…”